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41
votes
55
replies
11k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.7 years ago by midox ▴ 290
4
votes
45
replies
7.0k
views
SAM file wrong? help with validatesamfile
EXOME
updated 7 months ago by 41k • written 7.4 years ago by ▴ 110
19
votes
43
replies
5.0k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.3 years ago by nazaninhoseinkhan ▴ 510
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 19 months ago by 41k • written 8.8 years ago by ▴ 920
17
votes
37
replies
4.2k
views
No alias or index file found for protein database
next-gen software error sequence
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 500
5
votes
35
replies
3.0k
views
Reduce set of chromosomes in Pangenome graph
pangenome vg
updated 4 months ago by ▴ 410 • written 5 months ago by • 0
3
votes
32
replies
3.0k
views
fastqc report for degradome reads
fastqc adaptor
5.6 years ago by Sam ▴ 150
4
votes
30
replies
2.0k
views
Script makes different file then the manual command, but the command is the same
pipeline linux awk
3.4 years ago by stan.aanhane ▴ 30
14
votes
30
replies
3.0k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
4.6 years ago by Malka ▴ 80
4
votes
30
replies
2.0k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp indels vcf calls mpileup
updated 3.3 years ago by 41k • written 3.3 years ago by ▴ 30
8
votes
30
replies
4.5k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 3.7 years ago by ▴ 550 • written 3.7 years ago by ▴ 20
7
votes
29
replies
2.2k
views
What's the powerful biological methods for significant genes selection?
gene selection significant biological method R
5.0 years ago by Chaimaa ▴ 260
0
votes
29
replies
2.6k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.5 years ago by 20 • written 5.6 years ago by ▴ 20
11
votes
29
replies
9.0k
views
SummarizedExperiment nrow differs from ncol
DESeq2 SummarizedExperiment
updated 2.1 years ago by 41k • written 9.5 years ago by ★ 1.6k
2
votes
28
replies
6.7k
views
Memory use in indexing
Assembly software error
updated 5.3 years ago by 41k • written 5.5 years ago by ▴ 690
12
votes
28
replies
2.4k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
5.5 years ago by Za ▴ 140
4
votes
27
replies
4.0k
views
MISO test run fails error of bam file was not found
RNA-Seq Assembly software error next-gen genome
updated 3.0 years ago by 20 • written 7.3 years ago by ▴ 10
3
votes
27
replies
5.2k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing NGS
updated 5.3 years ago by • 0 • written 5.5 years ago by ▴ 10
9
votes
27
replies
7.0k
views
How do I use Glimmer 3.02?
sequencing
updated 4.9 years ago by • 0 • written 5.7 years ago by ▴ 50
1
vote
26
replies
5.6k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP plink association analysis
4.8 years ago by kushagraprasad24 • 0
3
votes
26
replies
1.4k
views
6 follow
STAR Genome index Error
STAR
updated 8 weeks ago by 41k • written 8 weeks ago by • 0
10
votes
25
replies
3.2k
views
The interpretation of PCA
DESeq2 R PCA
updated 5.4 years ago by 20 • written 5.4 years ago by ▴ 140
8
votes
25
replies
2.6k
views
construction of a database
sql noSQL neo4j database
updated 8 months ago by 41k • written 2.5 years ago by ▴ 20
24
votes
25
replies
7.4k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
3.3 years ago by dpc ▴ 240
13
votes
24
replies
4.1k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 6.7 years ago by 136k • written 6.7 years ago by ▴ 480
0
votes
24
replies
3.2k
views
converting spaces to tabs in gtf files
NCBI
2.6 years ago by storm1907 ▴ 30
5
votes
24
replies
8.1k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF Plink
5.5 years ago by DanielC ▴ 160
11
votes
24
replies
4.9k
views
BWA mem skip orientation
assembly genome alignment next-gen
4.6 years ago by williamsbrian5064 ▴ 500
1
vote
23
replies
1.5k
views
Parse multifasta files based on a values in two columns in a metadata file
parse mutlifasta RefSeq database strain
3.2 years ago by jmwhitha • 0
6
votes
23
replies
2.6k
views
Could you help me set up a VCF filter?
genome software error VCF filter
5.4 years ago by Charlie2 ▴ 50
10
votes
23
replies
2.1k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast alignment gene
updated 6.0 years ago by 136k • written 6.0 years ago by ★ 3.4k
1
vote
23
replies
1.6k
views
FASTQ exctract ID's
fastq
4.0 years ago by User000 ▴ 690
11
votes
22
replies
3.6k
views
No significant DEG: A request to double check my commands for limma.
limma differential gene expression covariates
4.6 years ago by RNAseqer ▴ 250
23
votes
22
replies
45k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 12 months ago by • 0 • written 5.6 years ago by ▴ 250
5
votes
22
replies
3.1k
views
Differential analysis between two cell lines
R RNA-Seq edgeR differential analysis
5.4 years ago by Biologist ▴ 290
1
vote
22
replies
3.1k
views
Genome Index and Alignment- STAR
RNA-Seq genome alignment STAR
updated 5.0 years ago by 86k • written 5.0 years ago by • 0
2
votes
22
replies
1.9k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree linkage genetics
13 months ago by Joel Wallenius ▴ 180
4
votes
22
replies
4.1k
views
samtools coverage usage
NGS
updated 2.4 years ago by ★ 1.2k • written 2.4 years ago by ▴ 20
1
vote
22
replies
5.7k
views
how to use faSplit to split fasta into x files
next-gen faSplit sequence
5.1 years ago by olechnwin ▴ 60
5
votes
22
replies
7.1k
views
SVM for classified gene expression data
R svm microarray
updated 16 months ago by 41k • written 7.9 years ago by ▴ 50
13
votes
22
replies
10k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 6.2 years ago by 20 • written 6.4 years ago by ★ 1.3k
3
votes
22
replies
2.8k
views
Making RefSeq in Windows
refseq
7.3 years ago by Alireza Ebadi Tabrizi • 0
0
votes
22
replies
3.1k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
5.6 years ago by Muha0216 • 0
2
votes
21
replies
3.7k
views
Compute the correlations between submatrices
correlation R matrix foreach
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 300
16
votes
21
replies
1.9k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
7.2 years ago by Farbod ★ 3.4k
12
votes
21
replies
2.9k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP prs gwas PRSice Plink
updated 4.3 years ago by 20 • written 4.4 years ago by ▴ 30
6
votes
21
replies
2.5k
views
How to evaluate the similarity of genes between two sample
RNA-Seq differential
updated 5.2 years ago by 20 • written 5.3 years ago by ▴ 190
3
votes
21
replies
3.4k
views
Normalization agilent microarray data?
Microarray Normalization
updated 2.6 years ago by 41k • written 4.2 years ago by ▴ 70
0
votes
21
replies
2.3k
views
HTSeq-Count: no_feature too high?
htseq-count
13 months ago by sea.joson ▴ 10
1
vote
21
replies
2.5k
views
Center and scale RIN values for DESeq2?
deseq2 rin
3.3 years ago by randalljellis ▴ 90
1,000 results • Page 1 of 20
Recent Votes
BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity
Answer: Genotypes in vcf files
Answer: Tools or R / Python packages to perfom ML models
Comment: Tools or R / Python packages to perfom ML models
Comment: How can I amend the output of a DIAMOND python script?
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
A: How to add biological annotations using R
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Recent Replies
Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30
I would like to train ML models without using datasets with images. Specifically, I would like to use transcriptomic data. Is it still poss…
Answer: Tools or R / Python packages to perfom ML models by Michael 53k
How about TensorFlow? https://www.tensorflow.org/overview You can run the examples directly in Colab. This short introduction uses Ke…
Comment: In what case there are RR reads but no LL reads when detect inversions using IGV by Istvan Albert 99k
you should visualize the image as pairs (view-as-pairs) the image you show is not quite right, it is also important to note what gets color…
Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30
Hi, I'm more comfortable with R right now. I found the R package "mlr3", I don't know if you know of any others. I would appreciate it if y…
Comment: HTseq reports missing attribute name by Istvan Albert 99k
sounds like your genome file is not quite correct, you need to make sure it is in FASTA format all the way through, perhaps get it from a r…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ? by ATpoint 78k
I it was available then you would see entries there. Still, be aware that this is raw sequencing data, so it's not just a list of miRNAs. C…
Comment: Tools or R / Python packages to perfom ML models by rpolicastro 12k
R and Python have access to most ML methods, it's just a matter of learning either of the languages and then finding which libraries are po…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by ATpoint 78k
Seconding that. Is there anything else that you can use for QC, like some Trypan Blue stain of the cells right before loading the chip? Is …
Comment: Where is the index command? by Michael 53k
samtools index (like genral programs you install on your machine) should run without sudo, if it doesn't, you might want to check the acces…
Comment: Where is the index command? by Michael 53k
I didn't know you were using WSL. Possibly the damage you can do with that is limited to the WSL environment and the worst thing that can h…
Comment: Is bisulfite-seq data from different studies comparable with each other? by Basti ★ 1.8k
There is no general rule, what you can apply depends on the nature of each dataset you intend to integrate (tissue, condition, technique, s…
Comment: Where is the index command? by Michael 53k
Running this is always a good idea.
Answer: Salmon indices differences by ATpoint 78k
In theory the full genome decoy is the best since it includes the entire genome, hence decoying potential spurious mappings due to DNA cont…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ? by Nitin Narwade ★ 1.5k
You can directly ask authors but as it is still on bioRxiv I don't think they can share this data with you until it get published somewhere…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ? by abourrieau • 0
Thank you, I had thought about this possibility but I don't see where it is indicated on the NCBI website: : https://www.ncbi.nlm.nih.gov/b…
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